tomography/xdesign

@article{Gordon1970,
author = {Gordon, Richard and Bender, Robert and Herman, Gabor T.},
doi = {10.1016/0022-5193(70)90109-8},
isbn = {0022-5193 (Print)$\backslash$n0022-5193 (Linking)},
issn = {10958541},
journal = {Journal of Theoretical Biology},
month = {dec},
number = {3},
pages = {471--481},
pmid = {5492997},
title = {{Algebraic Reconstruction Techniques (ART) for three-dimensional electron microscopy and X-ray photography}},
url = {https://doi.org/10.1016/0022-5193(70)90109-8},
volume = {29},
year = {1970}
}


@article{Gilbert1972,
abstract = {A method of reconstruction (ART) has recently been proposed (Gordon, Bender {\&} Herman, 1970) which consists in iteratively changing a trial structure until its projections are consistent with the original projections of the unknown structure. It is shown that in general ART produces erroneous reconstructions. An alternative iterative method is proposed which will give correct reconstructions under certain conditions. One of the potential applications of this method is in determining the three-dimensional structure of objects from electron micrographs. {\textcopyright} 1972.},
author = {Gilbert, Peter},
doi = {10.1016/0022-5193(72)90180-4},
isbn = {0022-5193},
issn = {10958541},
journal = {Journal of Theoretical Biology},
pmid = {5070894},
title = {{Iterative methods for the three-dimensional reconstruction of an object from projections}},
year = {1972},
url = {https://doi.org/10.1016/0022-5193(72)90180-4}
}


@article{AlRaoush:03,
author  = {Al-Raoush R and Thompson K and Willson CS},
title   = {Comparison of network generation techniques for unconsolidated porous media},
journal = {Soil Science Society of America Journal},
volume  = {67},
number  = {6},
pages   = {1687--1700},
year    = {2003}
}

@article{Xia:14,
author  = {Xia C and Zhu K and Cao Y and Sun H and Kou B and Wang Y},
title   = {X-ray tomography study of the random packing structure of ellipsoids},
journal = {Soft Matter},
volume  = {10},
number  = {7},
pages   = {990--996},
year    = {2014}
}

@article{AlRaoush:05,
author  = {Al-Raoush R and Willson CS},
title   = {Extraction of physically realistic pore network properties from three-dimensional synchrotron X-ray microtomography images of unconsolidated porous media systems},
journal = {Journal of Hydrology},
volume  = {300},
number  = {1},
pages   = {44-64},
year    = {2005}
}

@article{Sufian:15,
author  = {A Sufian and AR Russell and AJ Whittle and M Saadatfar},
title   = {Pore shapes, volume distribution and orientations in monodisperse
granular assemblies},
journal = {Granular Matter},
volume  = {17},
number  = {6},
pages   = {727--742},
year    = {2015}
}

@inproceedings{loebich2007digital,
  title={Digital camera resolution measurement using sinusoidal Siemens stars},
  author={Loebich, Christian and Wueller, Dietmar and Klingen, Bruno and Jaeger, Anke},
  booktitle={Electronic Imaging 2007},
  pages={65020N--65020N},
  year={2007},
  organization={International Society for Optics and Photonics}
}

@article{Bergamaschi:fv5047,
author = "Bergamaschi, Antoine and Medjoubi, Kadda and Messaoudi, C{\'{e}}dric and Marco, Sergio and Somogyi, Andrea",
title = "{{\it MMX-I}: data-processing software for multimodal X-ray imaging and tomography}",
journal = "Journal of Synchrotron Radiation",
year = "2016",
volume = "23",
number = "3",
pages = "783--794",
month = "May",
doi = {10.1107/S1600577516003052},
url = {http://dx.doi.org/10.1107/S1600577516003052},
abstract = {A new multi-platform freeware has been developed for the processing and reconstruction of scanning multi-technique X-ray imaging and tomography datasets. The software platform aims to treat different scanning imaging techniques: X-ray fluorescence, phase, absorption and dark field and any of their combinations, thus providing an easy-to-use data processing tool for the X-ray imaging user community. A dedicated data input stream copes with the input and management of large datasets (several hundred GB) collected during a typical multi-technique fast scan at the Nanoscopium beamline and even on a standard PC. To the authors' knowledge, this is the first software tool that aims at treating all of the modalities of scanning multi-technique imaging and tomography experiments.},
keywords = {scanning multimodal X-ray imaging, scanning X-ray tomography, tomographic reconstruction, phase retrieval, scanning multimodal X-ray imaging, scanning X-ray tomography, tomographic reconstruction, phase retrieval},
}

@article{Hsieh:06,
author = "Hsieh, Jiang and Londt, John and Vass, Melissa and Li, Jay and Tang, Xiangyang and Okerlund, Darin",
title = "Step-and-shoot data acquisition and reconstruction for cardiac x-ray computed tomography",
journal = "Medical Physics",
year = "2006",
volume = "33",
number = "11",
pages = "4236-4248",
url = "http://scitation.aip.org/content/aapm/journal/medphys/33/11/10.1118/1.2361078",
doi = "http://dx.doi.org/10.1118/1.2361078"
}

@article{Beverley:16,
author={Beverley F Holman and Vesna Cuplov and Brian F Hutton and Ashley M Groves and Kris Thielemans},
title={The effect of respiratory induced density variations on non-TOF PET quantitation in the lung},
journal={Physics in Medicine and Biology},
volume={61},
number={8},
pages={3148},
url={http://stacks.iop.org/0031-9155/61/i=8/a=3148},
year={2016}
}

@article{Liu:12,
author = "Liu, Yijin and Meirer, Florian and Williams, Phillip A. and Wang, Junyue and Andrews, Joy C. and Pianetta, Piero",
title = "{{\it TXM-Wizard}: a program for advanced data collection~and evaluation in full-field transmission X-ray microscopy}",
journal = "Journal of Synchrotron Radiation",
year = "2012",
volume = "19",
number = "2",
pages = "281--287",
month = "Mar",
doi = {10.1107/S0909049511049144},
url = {http://dx.doi.org/10.1107/S0909049511049144},
abstract = {Transmission X-ray microscopy (TXM) has been well recognized as a powerful tool for non-destructive investigation of the three-dimensional inner structure of a sample with spatial resolution down to a few tens of nanometers, especially when combined with synchrotron radiation sources. Recent developments of this technique have presented a need for new tools for both system control and data analysis. Here a software package developed in MATLAB for script command generation and analysis of TXM data is presented. The first toolkit, the script generator, allows automating complex experimental tasks which involve up to several thousand motor movements. The second package was designed to accomplish computationally intense tasks such as data processing of mosaic and mosaic tomography datasets; dual-energy contrast imaging, where data are recorded above and below a specific X-ray absorption edge; and TXM X-ray absorption near-edge structure imaging datasets. Furthermore, analytical and iterative tomography reconstruction algorithms were implemented. The compiled software package is freely available.},
keywords = {X-ray microscopy, full-field, tomography, XANES imaging},
}

@article{Vogelgesang:16,
author = "Vogelgesang, Matthias and Farago, Tomas and Morgeneyer, Thilo F. and Helfen, Lukas and dos Santos Rolo, Tomy and Myagotin, Anton and Baumbach, Tilo",
title = "{Real-time image-content-based beamline control for smart 4D X-ray imaging}",
journal = "Journal of Synchrotron Radiation",
year = "2016",
volume = "23",
number = "5",
pages = "",
month = "Sep",
doi = {10.1107/S1600577516010195},
url = {http://dx.doi.org/10.1107/S1600577516010195},
abstract = {Real-time processing of X-ray image data acquired at synchrotron radiation facilities allows for smart high-speed experiments. This includes workflows covering parameterized and image-based feedback-driven control up to the final storage of raw and processed data. Nevertheless, there is presently no system that supports an efficient construction of such experiment workflows in a scalable way. Thus, here an architecture based on a high-level control system that manages low-level data acquisition, data processing and device changes is described. This system is suitable for routine as well as prototypical experiments, and provides specialized building blocks to conduct four-dimensional {\it in situ}, {\it in~vivo} and {\it operando} tomography and laminography.},
keywords = {control, tomography, laminography},
}

@article{Marchesini:16,
author = "Marchesini, Stefano and Krishnan, Hari and Shapiro, David A. and Perciano, Talita and Sethian, James A. and Daurer, Benedikt J. and Maia, Filipe R. N. C.",
title = "{SHARP: a distributed, GPU-based ptychographic solver}",
year = "2016",
doi = "10.1107/S1600576716008074",
journal = "Report LBNL-1003977"
}

@article{Agostinelli:01,
title = "An object oriented fully 3D tomography visual toolkit ",
journal = "Computer Methods and Programs in Biomedicine ",
volume = "65",
number = "1",
pages = "61 - 69",
year = "2001",
note = "",
issn = "0169-2607",
doi = "http://dx.doi.org/10.1016/S0169-2607(00)00101-2",
url = "http://www.sciencedirect.com/science/article/pii/S0169260700001012",
author = "Stefano Agostinelli and Gabriella Paoli",
abstract = "In this paper we present a modern object oriented component object model (COMM) C + + toolkit dedicated to fully 3D cone-beam tomography. The toolkit allows the display and visual manipulation of analytical phantoms, projection sets and volumetric data through a standard Windows graphical user interface. Data input/output is performed using proprietary file formats but import/export of industry standard file formats, including raw binary, Windows bitmap and AVI, ACR/NEMA \{DICOMM\} 3 and \{NCSA\} \{HDF\} is available. At the time of writing built-in implemented data manipulators include a basic phantom ray-tracer and a Matrox Genesis frame grabbing facility. A \{COMM\} plug-in interface is provided for user-defined custom backprojector algorithms: a simple Feldkamp ActiveX control, including source code, is provided as an example; our fast Feldkamp plug-in is also available. "
}

@article{Bayford:95,
  author={R Bayford and Y Hanquan and K Boone and D S Holder},
  title={Experimental validation of a novel reconstruction algorithm for electrical impedance tomography based on backprojection of Lagrange multipliers},
  journal={Physiological Measurement},
  volume={16},
  number={3A},
  pages={A237},
  url={http://stacks.iop.org/0967-3334/16/i=3A/a=022},
  year={1995},
  abstract={A novel approach to image reconstruction for electrical impedance tomography (EIT) has been developed. It is based on a constrained optimization technique for the reconstruction of difference resistivity images without finite-element modelling. It solves the inverse problem by optimizing a cost function under constraints, in the form of normalized boundary potentials. Its application to the neighbouring data collection method is presented here. Mathematical models are developed according to specified criteria. These express the reconstructed image in terms of one-dimensional Lagrange multiplier functions. The reconstruction problem becomes one of estimating these functions from normalized boundary potentials. This model is based on a cost criterion of the minimization of the variance between the reconstructed and the true resistivity distributions. The algorithm was tested on data collected in a cylindrical saline-filled tank. A polyacrylamide rod was placed in various positions with or without a peripheral plaster of Paris ring in place. This was intended to resemble the conditions during EIT of epileptic seizures recorded with scalp or cortical electrodes in the human head. One advantage of this approach is that compensation for non-uniform initial conditions may be made, as this is a significant problem in imaging cerebral activity through the skull.}
}

@article{Chaâri:11,
title = "A wavelet-based regularized reconstruction algorithm for \{SENSE\} parallel \{MRI\} with applications to neuroimaging ",
journal = "Medical Image Analysis ",
volume = "15",
number = "2",
pages = "185 - 201",
year = "2011",
note = "",
issn = "1361-8415",
doi = "http://dx.doi.org/10.1016/j.media.2010.08.001",
url = "http://www.sciencedirect.com/science/article/pii/S1361841510001052",
author = "Lotfi Chaâri and Jean-Christophe Pesquet and Amel Benazza-Benyahia and Philippe Ciuciu",
abstract = "To reduce scanning time and/or improve spatial/temporal resolution in some Magnetic Resonance Imaging (MRI) applications, parallel \{MRI\} acquisition techniques with multiple coils acquisition have emerged since the early 1990s as powerful imaging methods that allow a faster acquisition process. In these techniques, the full \{FOV\} image has to be reconstructed from the resulting acquired undersampled k-space data. To this end, several reconstruction techniques have been proposed such as the widely-used \{SENSitivity\} Encoding (SENSE) method. However, the reconstructed image generally presents artifacts when perturbations occur in both the measured data and the estimated coil sensitivity profiles. In this paper, we aim at achieving accurate image reconstruction under degraded experimental conditions (low magnetic field and high reduction factor), in which neither the \{SENSE\} method nor the Tikhonov regularization in the image domain give convincing results. To this end, we present a novel method for SENSE-based reconstruction which proceeds with regularization in the complex wavelet domain by promoting sparsity. The proposed approach relies on a fast algorithm that enables the minimization of regularized non-differentiable criteria including more general penalties than a classical ℓ1 term. To further enhance the reconstructed image quality, local convex constraints are added to the regularization process. In vivo human brain experiments carried out on Gradient-Echo (GRE) anatomical and Echo Planar Imaging (EPI) functional \{MRI\} data at 1.5 T indicate that our algorithm provides reconstructed images with reduced artifacts for high reduction factors. "
}

@ARTICLE{Dean-Ben:12,
author={X. L. Dean-Ben and A. Buehler and V. Ntziachristos and D. Razansky},
journal={IEEE Transactions on Medical Imaging},
title={Accurate Model-Based Reconstruction Algorithm for Three-Dimensional Optoacoustic Tomography},
year={2012},
volume={31},
number={10},
pages={1922-1928},
keywords={acoustic tomography;biomedical ultrasonics;image reconstruction;image resolution;medical image processing;optical tomography;phantoms;1D scanning geometry;3D optoacoustic tomography;backprojection inversion algorithm;dimensionality;image contrast loss;image reconstruction;image spatial resolution;imaging speed;model based reconstruction algorithm;out-of-plane image artifacts;phantom;Absorption;Computational modeling;Image reconstruction;Phantoms;Tomography;Transducers;Model-based reconstruction;optoacoustic tomography;photoacoustic tomography;three-dimensional imaging;Algorithms;Animals;Computer Simulation;Heart;Imaging, Three-Dimensional;Mice;Models, Theoretical;Phantoms, Imaging;Photoacoustic Techniques;Tomography},
doi={10.1109/TMI.2012.2208471},
ISSN={0278-0062},
month={Oct},}

@article{Dobbins:95,
author = "Dobbins, James T.",
title = "Effects of undersampling on the proper interpretation of modulation transfer function, noise power spectra, and noise equivalent quanta of digital imaging systems",
journal = "Medical Physics",
year = "1995",
volume = "22",
number = "2",
pages = "171-181",
url = "http://scitation.aip.org/content/aapm/journal/medphys/22/2/10.1118/1.597600",
doi = "http://dx.doi.org/10.1118/1.597600"
}

@article{Friedman:13,
author = "Friedman, Saul N. and Fung, George S. K. and Siewerdsen, Jeffrey H. and Tsui, Benjamin M. W.",
title = "A simple approach to measure computed tomography (CT) modulation transfer function (MTF) and noise-power spectrum (NPS) using the American College of Radiology (ACR) accreditation phantom",
journal = "Medical Physics",
year = "2013",
volume = "40",
number = "5",
eid = 051907,
pages = "",
url = "http://scitation.aip.org/content/aapm/journal/medphys/40/5/10.1118/1.4800795",
doi = "http://dx.doi.org/10.1118/1.4800795"
}

@article{Han:12,
author = "B. Kelly Han and Katharine L.R. Grant and Ross Garberich and Martin Sedlmair and Jana Lindberg and John R. Lesser",
title = "Assessment of an iterative reconstruction algorithm (SAFIRE) on image quality in pediatric cardiac \{CT\} datasets ",
journal = "Journal of Cardiovascular Computed Tomography ",
volume = "6",
number = "3",
pages = "200 - 204",
year = "2012",
note = "",
issn = "1934-5925",
doi = "http://dx.doi.org/10.1016/j.jcct.2012.04.008",
url = "http://www.sciencedirect.com/science/article/pii/S1934592512001402",
}

@article{Hsieh:04,
   author = "Hsieh, J. and Chao, E. and Thibault, J. and Grekowicz, B. and Horst, A. and McOlash, S. and Myers, T. J.",
   title = "A novel reconstruction algorithm to extend the CT scan field-of-view",
   journal = "Medical Physics",
   year = "2004",
   volume = "31",
   number = "9",
   pages = "2385-2391",
   url = "http://scitation.aip.org/content/aapm/journal/medphys/31/9/10.1118/1.1776673",
   doi = "http://dx.doi.org/10.1118/1.1776673"
}

@Article{Hunter:07,
  Author    = {Hunter, J. D.},
  Title     = {Matplotlib: A 2D graphics environment},
  Journal   = {Computing In Science \& Engineering},
  Volume    = {9},
  Number    = {3},
  Pages     = {90--95},
  abstract  = {Matplotlib is a 2D graphics package used for Python
  for application development, interactive scripting, and
  publication-quality image generation across user
  interfaces and operating systems.},
  publisher = {IEEE COMPUTER SOC},
  year      = 2007
}

@article{Jan:04,
  author={S Jan and G Santin and D Strul and S Staelens and K Assié and D Autret and S Avner and R Barbier and M Bardiès and P M Bloomfield and D
Brasse and V Breton and P Bruyndonckx and I Buvat and A F Chatziioannou and Y Choi and Y H Chung and C Comtat and D Donnarieix and L
Ferrer and S J Glick and C J Groiselle and D Guez and P-F Honore and S Kerhoas-Cavata and A S Kirov and V Kohli and M Koole and M
Krieguer and D J van der Laan and F Lamare and G Largeron and C Lartizien and D Lazaro and M C Maas and L Maigne and F Mayet and F
Melot and C Merheb and E Pennacchio and J Perez and U Pietrzyk and F R Rannou and M Rey and D R Schaart and C R Schmidtlein and L
Simon and T Y Song and J-M Vieira and D Visvikis and R Van de Walle and E Wieërs and C Morel},
  title={GATE: a simulation toolkit for PET and SPECT},
  journal={Physics in Medicine and Biology},
  volume={49},
  number={19},
  pages={4543},
  url={http://stacks.iop.org/0031-9155/49/i=19/a=007},
  year={2004},
  abstract={Monte Carlo simulation is an essential tool in emission tomography that can assist in the design of new medical imaging devices, the optimization of acquisition protocols and the development or assessment of image reconstruction algorithms and correction techniques. GATE, the Geant4 Application for Tomographic Emission, encapsulates the Geant4 libraries to achieve a modular, versatile, scripted simulation toolkit adapted to the field of nuclear medicine. In particular, GATE allows the description of time-dependent phenomena such as source or detector movement, and source decay kinetics. This feature makes it possible to simulate time curves under realistic acquisition conditions and to test dynamic reconstruction algorithms. This paper gives a detailed description of the design and development of GATE by the OpenGATE collaboration, whose continuing objective is to improve, document and validate GATE by simulating commercially available imaging systems for PET and SPECT. Large effort is also invested in the ability and the flexibility to model novel detection systems or systems still under design. A public release of GATE licensed under the GNU Lesser General Public License can be downloaded at http://www-lphe.epfl.ch/GATE/ [http://www-lphe.epfl.ch/GATE/] . Two benchmarks developed for PET and SPECT to test the installation of GATE and to serve as a tutorial for the users are presented. Extensive validation of the GATE simulation platform has been started, comparing simulations and measurements on commercially available acquisition systems. References to those results are listed. The future prospects towards the gridification of GATE and its extension to other domains such as dosimetry are also discussed.}
}

@ARTICLE{Kostli:01,
author={K. P. Kostli and D. Frauchiger and J. J. Niederhauser and G. Paltauf and H. P. Weber and M. Frenz},
journal={IEEE Journal of Selected Topics in Quantum Electronics},
title={Optoacoustic imaging using a three-dimensional reconstruction algorithm},
year={2001},
volume={7},
number={6},
pages={918-923},
keywords={acoustic tomography;biomedical ultrasonics;fast Fourier transforms;image reconstruction;inverse problems;medical image processing;photoacoustic effect;2-D pressure distributions;3-D optoacoustic images;Fourier-reconstruction algorithm;Green's function;Poisson integral;backprojection;blood vessel model;decomposition into plane waves;fast Fourier algorithm;forward problem;four-dimensional space-time;gated CCD camera;insect body;intensity changes;inverse problem;medical diagnostics;optical pressure transducer;optoacoustic imaging;reflected probe beam;sample surface;simulated pressure transients;three-dimensional reconstruction algorithm;tomography images;Delay;Distributed computing;Image reconstruction;Image resolution;Laser excitation;Optical pulses;Pressure measurement;Pulse measurements;Surface reconstruction;Two dimensional displays},
doi={10.1109/2944.983294},
ISSN={1077-260X},
month={Nov},}

@article{Köhler:11,
   author = "Köhler, Thomas and Brendel, Bernhard and Roessl, Ewald",
   title = "Iterative reconstruction for differential phase contrast imaging using spherically symmetric basis functions",
   journal = "Medical Physics",
   year = "2011",
   volume = "38",
   number = "8",
   pages = "4542-4545",
   url = "http://scitation.aip.org/content/aapm/journal/medphys/38/8/10.1118/1.3608906",
   doi = "http://dx.doi.org/10.1118/1.3608906"
}

@article{Kumar:15,
   author = "Kumar, Arjun S. and Mandal, Pratiti and Zhang, Yongjie and Litster, Shawn",
   title = "Image segmentation of nanoscale Zernike phase contrast X-ray computed tomography images",
   journal = "Journal of Applied Physics",
   year = "2015",
   volume = "117",
   number = "18",
   eid = 183102,
   pages = "",
   url = "http://scitation.aip.org/content/aip/journal/jap/117/18/10.1063/1.4919835",
   doi = "http://dx.doi.org/10.1063/1.4919835"
}

@article{Marone:12,
author = "Marone, F. and Stampanoni, M.",
title = "{Regridding reconstruction algorithm for real-time tomographic imaging}",
journal = "Journal of Synchrotron Radiation",
year = "2012",
volume = "19",
number = "6",
pages = "1029--1037",
month = "Nov",
doi = {10.1107/S0909049512032864},
url = {http://dx.doi.org/10.1107/S0909049512032864},
abstract = {Sub-second temporal-resolution tomographic microscopy is becoming a reality at third-generation synchrotron sources. Efficient data handling and post-processing is, however, difficult when the data rates are close to 10GBs${\sp {$-$}1}$. This bottleneck still hinders exploitation of the full potential inherent in the ultrafast acquisition speed. In this paper the fast reconstruction algorithm {\it gridrec}, highly optimized for conventional CPU technology, is presented. It is shown that {\it gridrec} is a valuable alternative to standard filtered back-projection routines, despite being based on the Fourier transform method. In fact, the regridding procedure used for resampling the Fourier space from polar to Cartesian coordinates couples excellent performance with negligible accuracy degradation. The stronger dependence of the observed signal-to-noise ratio for {\it gridrec} reconstructions on the number of angular views makes the presented algorithm even superior to filtered back-projection when the tomographic problem is well sampled. {\it Gridrec} not only guarantees high-quality results but it provides up to 20-fold performance increase, making real-time monitoring of the sub-second acquisition process a reality.},
keywords = {tomographic reconstruction, fast algorithm, Fourier method, regridding, PSWF},
}

@inproceedings{palenstijn:13,
  title={The ASTRA tomography toolbox},
  author={Palenstijn, Willem Jan and Batenburg, K Joost and Sijbers, Jan},
  booktitle={13th International Conference on Computational and Mathematical Methods in Science and Engineering, CMMSE},
  volume={2013},
  year={2013}
}

@article{roy:05,
  title={Tomographic fluorescence imaging in tissue phantoms: a novel reconstruction algorithm and imaging geometry},
  author={Roy, Ranadhir and Thompson, Alan B and Godavarty, Anuradha and Sevick-Muraca, Eva M},
  journal={IEEE transactions on medical imaging},
  volume={24},
  number={2},
  pages={137--154},
  year={2005},
  publisher={IEEE}
}

@ARTICLE{Sheikh:15,
author={H. R. Sheikh and A. C. Bovik},
journal={IEEE Transactions on Image Processing},
title={Image information and visual quality},
year={2006},
volume={15},
number={2},
pages={430-444},
keywords={image enhancement;visual perception;distorted image;human visual system;image information;image quality;quality assessment;signal fidelity measures;visual information fidelity;visual quality;Algorithm design and analysis;Distortion measurement;Humans;Image quality;Predictive models;Psychology;Quality assessment;Statistics;Video sharing;Visual system;Image information;image quality assessment (QA);information fidelity;natural scene statistics (NSS);Algorithms;Artificial Intelligence;Biomimetics;Humans;Image Enhancement;Image Interpretation, Computer-Assisted;Information Storage and Retrieval;Reproducibility of Results;Sensitivity and Specificity},
doi={10.1109/TIP.2005.859378},
ISSN={1057-7149},
month={Feb},}


@article{Thielemans:12,
  author={Kris Thielemans and Charalampos Tsoumpas and Sanida Mustafovic and Tobias Beisel and Pablo Aguiar and Nikolaos
Dikaios and Matthew W Jacobson},
  title={STIR: software for tomographic image reconstruction release 2},
  journal={Physics in Medicine and Biology},
  volume={57},
  number={4},
  pages={867},
  url={http://stacks.iop.org/0031-9155/57/i=4/a=867},
  year={2012},
  abstract={We present a new version of STIR ( Software for Tomographic Image Reconstruction ), an open source object-oriented library implemented in C++ for 3D positron emission tomography reconstruction. This library has been designed such that it can be used for many algorithms and scanner geometries, while being portable to various computing platforms. This second release enhances its flexibility and modular design and includes additional features such as Compton scatter simulation, an additional iterative reconstruction algorithm and parametric image reconstruction (both indirect and direct). We discuss the new features in this release and present example results. STIR can be downloaded from http://stir.sourceforge.net [http://stir.sourceforge.net] .}
}

@article{Treeby:10,
author = {Treeby, Bradley E. and Cox, B. T.},
title = {k-Wave: MATLAB toolbox for the simulation and reconstruction of photoacoustic wave fields},
journal = {Journal of Biomedical Optics},
volume = {15},
number = {2},
pages = {021314-021314-12},
abstract = {A new, freely available third party MATLAB toolbox for the simulation and reconstruction of photoacoustic wave fields is described. The toolbox, named k-Wave, is designed to make realistic photoacoustic modeling simple and fast. The forward simulations are based on a k-space pseudo-spectral time domain solution to coupled first-order acoustic equations for homogeneous or heterogeneous media in one, two, and three dimensions. The simulation functions can additionally be used as a flexible time reversal image reconstruction algorithm for an arbitrarily shaped measurement surface. A one-step image reconstruction algorithm for a planar detector geometry based on the fast Fourier transform (FFT) is also included. The architecture and use of the toolbox are described, and several novel modeling examples are given. First, the use of data interpolation is shown to considerably improve time reversal reconstructions when the measurement surface has only a sparse array of detector points. Second, by comparison with one-step, FFT-based reconstruction, time reversal is shown to be sufficiently general that it can also be used for finite-sized planar measurement surfaces. Last, the optimization of computational speed is demonstrated through parallel execution using a graphics processing unit.},
year = {2010},
isbn = {1083-3668},
doi = {10.1117/1.3360308},
URL = { http://dx.doi.org/10.1117/1.3360308},
eprint = {}
}

@inproceedings{wang:03,
  title={Multiscale structural similarity for image quality assessment},
  author={Wang, Zhou and Simoncelli, Eero P and Bovik, Alan C},
  booktitle={Signals, Systems and Computers, 2004. Conference Record of the Thirty-Seventh Asilomar Conference on},
  volume={2},
  pages={1398--1402},
  year={2003},
  organization={Ieee}
}

@article{wang:06,
  title={Modern image quality assessment},
  author={Wang, Zhou and Bovik, Alan C},
  journal={Synthesis Lectures on Image, Video, and Multimedia Processing},
  volume={2},
  number={1},
  pages={1--156},
  year={2006},
  publisher={Morgan \& Claypool Publishers}
}

@article{wang:02,
  title={A universal image quality index},
  author={Wang, Zhou and Bovik, Alan C},
  journal={IEEE signal processing letters},
  volume={9},
  number={3},
  pages={81--84},
  year={2002},
  publisher={IEEE}
}

@article{Wu:13,
title = "A phase retrieval algorithm for X-ray phase contrast imaging ",
journal = "Optik - International Journal for Light and Electron Optics ",
volume = "124",
number = "9",
pages = "864 - 866",
year = "2013",
note = "",
issn = "0030-4026",
doi = "http://dx.doi.org/10.1016/j.ijleo.2012.02.030",
url = "http://www.sciencedirect.com/science/article/pii/S0030402612001635",
author = "Jie Wu and Jiabi Chen",
abstract = "Based on the transport-of-intensity equation and the Fourier transform, a rapid phase retrieval algorithm for X-ray phase contrast imaging is described in detail. This algorithm is a non-iterative phase retrieval method, and it has a potential speed for large scale X-ray phase contrast images. Then the numerical simulation is made to evaluate the rapid phase retrieval algorithm performance. Finally, a real fiber material experiment is carried out using a micro focus X-ray phase contrast imaging experiment platform, and the phase distribution image is calculated out by this algorithm. The result shows that this phase retrieval algorithm is effective and optional to practical application. "
}

@article{Yin:12,
title = "Understanding the phase contrast optics to restore artifact-free microscopy images for segmentation ",
journal = "Medical Image Analysis ",
volume = "16",
number = "5",
pages = "1047 - 1062",
year = "2012",
note = "",
issn = "1361-8415",
doi = "http://dx.doi.org/10.1016/j.media.2011.12.006",
url = "http://www.sciencedirect.com/science/article/pii/S1361841512000035",
author = "Zhaozheng Yin and Takeo Kanade and Mei Chen",
abstract = "Phase contrast, a noninvasive microscopy imaging technique, is widely used to capture time-lapse images to monitor the behavior of transparent cells without staining or altering them. Due to the optical principle, phase contrast microscopy images contain artifacts such as the halo and shade-off that hinder image segmentation, a critical step in automated microscopy image analysis. Rather than treating phase contrast microscopy images as general natural images and applying generic image processing techniques on them, we propose to study the optical properties of the phase contrast microscope to model its image formation process. The phase contrast imaging system can be approximated by a linear imaging model. Based on this model and input image properties, we formulate a regularized quadratic cost function to restore artifact-free phase contrast images that directly correspond to the specimen’s optical path length. With artifacts removed, high quality segmentation can be achieved by simply thresholding the restored images. The imaging model and restoration method are quantitatively evaluated on microscopy image sequences with thousands of cells captured over several days. We also demonstrate that accurate restoration lays the foundation for high performance in cell detection and tracking. "
}

@article{zanaga:16,
title={Quantitative 3D analysis of huge nanoparticle assemblies},
author={Zanaga, Daniele and Bleichrodt, Folkert and Altantzis, Thomas and Winckelmans, Naomi and Palenstijn, Willem Jan and Sijbers, Jan and de Nijs, Bart and van Huis, Marijn A and S{\'a}nchez-Iglesias, Ana and Liz-Marz{\'a}n, Luis M and others},
journal={Nanoscale},
volume={8},
number={1},
pages={292--299},
year={2016},
publisher={Royal Society of Chemistry}
}

@article{zhang:11,
  title={FSIM: a feature similarity index for image quality assessment},
  author={Zhang, Lin and Zhang, Lei and Mou, Xuanqin and Zhang, David},
  journal={IEEE transactions on Image Processing},
  volume={20},
  number={8},
  pages={2378--2386},
  year={2011},
  publisher={IEEE}
}